Modified lipopolysaccharide glycoform and method of use

ABSTRACT

The present disclosure generally relates to genetic engineering of bacteria. More particularly, the present disclosure describes genetic engineering of  E. coli  to create mutant O-antigen ligase, as well as novel lipopolysaccharide molecules resulting from that genetic engineering. Methods for using those novel molecules are also described.

CROSS-REFERENCE TO PRIOR FILED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/991,116, filed May 9, 2014, and U.S. Provisional Application No.62/098,014, filed Dec. 30, 2014, which are incorporated herein in theirentirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under Grant No. GM034821awarded by the National Institutes of Health. The government has certainrights in this invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Apr. 27, 2015, isnamed PRINCETON-37203_SL.txt and is 7,622 bytes in size.

BACKGROUND OF THE INVENTION

A peptidoglycan (PG) cell wall is an essential extracytoplasmic featureof most bacteria (Singer et al., 1989); this essentiality has made itsbiogenesis a fruitful target for antibiotics, including vancomycin andpenicillin. The cell wall is directly exposed to the extracellularmilieu in Gram-positive bacteria, but is shielded in Escherichia coli(E. coli) and other Gram-negative species by a highly selectivepermeability barrier formed by the outer membrane (OM). The OM preventsinflux of antibiotics, such as vancomycin, restricting their access tointracellular targets (Eggert et al., 2001; Ruiz et al., 2005).

Lipopolysaccharide (LPS) forms the surface-exposed outer leaflet of theOM and is key to the barrier function (Osborn et al., 1972; Kamio andNikaido, 1976; Nikaido, 2003). LPS is a glycolipid consisting of a‘lipid A’ anchor within the bilayer, and a set of covalently attacheddistal ‘core’ saccharides (Raetz and Whitfield, 2002). LPS is made atthe cytosolic leaflet of the inner membrane (IM) before being flipped tothe periplasmic leaflet (Zhou et al., 1998). A transenvelope complex ofseven lipopolysaccharide transport proteins (LptABCDEFG) delivers LPSfrom the IM to the OM (Ruiz et al., 2009; Chng, Gronenberg, et al.,2010). A sub-complex of the β-barrel LptD and lipoprotein LptE resideswithin the OM and accomplishes the final step of inserting LPS into theouter leaflet (Chng, Ruiz, et al., 2010).

LPS and PG are both potent activators of immune responses via distinctstimulatory mechanisms. However, LPS is inherently toxic to humans andanimals due to hyper-activation of inflammatory immune responses.Detoxification can eliminate some or all of the endotoxicity, but theless toxic variants generally also have reduced immunostimulatoryproperties. LPS-stimulated immune responses can be synergisticallyincreased by co-stimulation with PG added into a mixture (Fritz et al.,2005). Therefore, this synergy is likely to be improved by directcoupling of LPS and PG into a single molecule that allows bothactivators to stimulate their associated pathways. A detoxified LPS-PGmolecule will likely retain more desirable immunostimulatory propertiesin comparison to detoxified LPS alone.

BRIEF SUMMARY OF THE INVENTION

Mutant O-antigen ligases are disclosed. It includes isolated proteinsthat have the amino acid sequence SEQ ID NO: 1, or isolated proteinshaving at least 90% sequence identity to SEQ ID NO: 2 and having anamino acid substitution of phenylalanine to serine at the phenylalaninehomologous to position 332 of SEQ ID NO: 2. A vaccine adjuvant may alsobe produced from a lipopolysaccharide or a lipopolysaccharide derivativeisolated from a mutant O-antigen ligase. A polynucleotide may alsoencode a mutant O-antigen ligase.

A LPS glycoform modified with peptidoglycan cell wall fragments is alsodisclosed. The LPS glycoform may be adapted to displayantibiotic-specific binding sites at a cell surface, of which vancomycinis one such antibiotic. The LPS glycoform may be able to activatereceptors or signaling pathways within the human body, includingTRL4/MD2 NOD1, and NOD2 receptors, and the TRIF/TRAM pathways.

A bacterium that expresses a LPS glycoform is also disclosed. Thebacterium may include a gene encoding a mutant O-antigen ligase.

A method for creating an LPS molecule is also disclosed. An E. colistrain is provided that expresses a mutant O-antigen ligase, it isplaced in conditions allowing it to grow, and then the LPS molecule isisolated. The LPS molecule may be isolated by separating the moleculesbased on at least one of the group consisting of size, chemicalcomposition, and affinity for a particular binding agent.

A method for generating a LPS* derivative molecule is also disclosed. AnE. coli strain is provided that expresses a LPS derivative moleculehaving reduced endotoxicity, modifying the E. coli strain by creating amutant O-antigen ligase, and placing it in conditions allowing it togrow and produce the LPS* molecule. The LPS* derivative molecule may beisolated at that time. The LPS derivative molecule may be3-O-deacyl-4′-monophosphoryl lipid A. A vaccine adjuvant may also becreated, comprising the LPS* derivative molecule.

A modified LPS molecule having at least one non-native sugar and agreater molecular weight as compared to the LPS molecule it is modifiedfrom is also disclosed.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows analysis of various strains utilizing one aspect of theinvention with regards to vancomycin resistance.

FIG. 2 shows analysis of one aspect of the invention with regards toresistance to two alternate antibiotics.

FIGS. 3-4 shows the SDS-PAGE analysis of LPS molecules from variousstrains.

FIG. 5 shows analysis of various strains utilizing one aspect of theinvention with regards to vancomycin resistance.

FIG. 6 shows the structure of Lipid II and schematic of peptidoglycancleavage by mutanolysin that releases pentapeptide (“A”) andtetrapeptide (“B”) species.

FIG. 7 shows analysis indicating waaL15 isolate LPS treated withmutanolysin cleaves the LPS* modification.

FIG. 8 shows total ion chromatograms for degradation products of LPS andLPS*, and a total ion chromatogram for LPS* degradation.

FIG. 9 shows the equilibrium signal of the reference subtracted SPRbinding kinetics at 25° C.

FIG. 10 shows the SPR binding kinetics at 25° C. of variousconcentrations of vancomycin passing over surfaces of total isolated LPSfrom waaL+.

FIG. 11 shows the SPR binding kinetics at 25° C. of variousconcentrations of vancomycin passing over surfaces of total isolated LPSfrom waaL15.

FIG. 12 shows the reference subtracted SPR binding kinetics at 25° C.

FIG. 13 shows fluorescence microscopy images of waaL+ and waal15.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure generally relates to the genetic engineering ofbacteria. More particularly, the present disclosure relates to geneticengineering of a gram-negative bacteria expressing a modified LPSmolecule, and methods for making and using the molecule.

While the present disclosure is susceptible to various modifications andalternative forms, specific example embodiments are herein described inmore detail. It should be understood, however, that the description ofspecific example embodiments is not intended to limit the invention tothe particular forms disclosed. The features and advantages of thepresent invention will be apparent to those skilled in the art. Whilenumerous changes may be made by those skilled in the art, such changesare within the spirit of the invention.

A recently described lptE mutation (lptE613) causes defective LPStransport and leads to increased antibiotic sensitivity (Malojĉić etal., 2014). In certain aspects of the invention, an isolatedvancomycin-resistant strain of E. coli carrying a F332S substitution inthe O-antigen ligase gene (waaL) and capable of restoring vancomycinresistance was isolated and characterized (See FIG. 1).

One embodiment of this invention increases vancomycin resistance instrains carrying bamB or bamE null mutations that disrupt the OM barrierby causing defects in β-barrel protein assembly (See FIG. 1). Certainembodiments of the invention also increase vancomycin-resistance acrossdifferent strains, including the wild-type strain (See FIG. 1).

The domesticated E. coli K-12 does not produce the normal substrate(O-Ag) of waaL (Liu and Reeves, 1994) and a waaL deletion does notsuppress vancomycin sensitivity, indicating that waaL15 is a gain offunction mutation. Thus, certain aspects of the embodied invention musthave an altered activity. Silver-staining of isolated LPS confirmed thatwaaL15 modifies LPS with additional sugars to produce one embodiment ofthis invention, a novel glycoform (LPS* herein), detected as a highermolecular weight band that is absent in waaL+ (See FIG. 3).

WaaL can use two minor saccharide substrates to modify LPS in E. coliK-12: enterobacterial common-antigen (ECA) and colanic acid (CA).ECA-modified LPS is a minor constituent of the OM (Schmidt et al., 1976;Meredith et al., 2007). Production of CA is regulated by the Rcsphospho-relay stress response system, and CA-modified LPS (called‘M-LPS’) is only detectable during severe envelope stress (Meredith etal., 2007). LPS silver-staining revealed that LPS* remained detectablefollowing inactivation of biosynthesis of ECA (rff), CA (cpsG), or boththese polysaccharides (rff cpsG) (See FIG. 3). Increasing the amounts ofa competing substrate by introducing the resC137 mutation to activateexpression of the genes for CA biosynthesis (Gottesman et al., 1985),lowered LPS* abundance at the expense of increased M-LPS (See FIG. 4).The decrease in LPS* correlated with a significant reduction invancomycin-resistance, indicating that LPS* molecules directly mediatethe resistance (FIG. 5). WaaL15 is able to use a new substrate andthereby generate a previously uncharacterized LPS glycoform thatprovides a specific mechanism for vancomycin resistance.

All native WaaL substrates contain carbohydrates linked to a commonundecaprenyl (Und) lipid carrier. PG biosynthesis involves adisaccharide pentapeptide (DPP) linked to the same Und carrier, amolecule called lipid II (See FIG. 6). Isolated LPS* was treated withthe muralytic enzyme mutanolysin (See FIGS. 6 and 7). Digestion ofpurified LPS*, but not LPS, liberated near-stoichiometric quantities offragments that were identified by mass spectrometry as DPP orderivatives with a tetrapeptide stem (See FIG. 8). There was no evidencefor cross-linked products suggesting that lipid II was the source of theLPS* glycosylation.

There are several carboxypeptidases in the periplasm that remove theterminal D-Alanine (D-Ala) from DPP to produce the tetrapeptidederivative. Indeed, E. coli PG contains negligible amounts ofpentapeptide stems. FIG. 8 shows that, in at least one instance, about50% of the LPS* is sequestered before it can be attacked by one of thesecarboxypeptidases. It is expected that sequestration occurs because themolecule is transported from the periplasm to the cell surface.

Peptide stems from adjacent peptidoglycan strands in the cell wall arecross-linked via transpeptidation between the penultimate D-Ala on onestem and a meso-diaminopimelic acid(m-DAP) residue on a nearby stem(Vollmer et al., 2008).

Extensive cross-linking produces a rigid macromolecular meshwork that isvital to cell wall function. Vancomycin binds and sequesters theterminal D-Ala-D-Ala residues of a pentapeptide stem in order to inhibittranspeptidation (Perkins, 1969). Since LPS* was the product of DPPligation onto LPS, this modified glycoform should contain vancomycinbinding sites.

Several vancomycin-resistance mechanisms exist in Gram-positivebacteria, including: alterations in peptidoglycan metabolism can producethicker cell walls (Cui et al., 2003); and transpeptidation can bereduced to leave more free D-Ala-D-Ala residues within the establishedcell wall structure (Sieradzki and Tomasz, 1997). In one aspect of theinvention, it has been shown that the waaL15 mechanism is comparablesince it also increases the number of free D-Ala-D-Ala targets that cantie up vancomycin. Moreover, by displaying D-Ala-D-Ala at the cellsurface the waaL15 mutation titrates vancomycin away from the true drugtarget, in an altogether different cellular compartment. Therefore,certain embodiments of the invention confer resistance by acting as amolecular decoy for vancomycin.

It should be understood by those skilled in the art that in certainother embodiments, the present disclosure may provide improved deliveryof vaccines or improved vaccine adjuvants derived from the LPS* moleculeof the present invention.

The biosynthesis of LPS* is remarkable. Lipid II in E. coli is extremelyscarce, its steady-state abundance is thought to be only 1,000-2,000molecules per cell (van Heijenoort et al., 1992). Insertion of new PG isthought to occur via large multiprotein morphogenic complexes: theelongasome and the divisome, responsible for PG synthesis along thelateral cell body and at the septum, respectively. In order to overcomethe scarcity of lipid II and limit its diffusion away from sites of PGgrowth, both complexes are suggested to include at least some of thelipid II biosynthetic enzymes, and the presumed flippases that deliverlipid II from the site of synthesis in the cytoplasm to the site of cellwall assembly in the periplasm (Szwedziak and Löwe, 2013). In thismodel, the substrate for PG synthesis would be isolated physically fromthe LPS assembly pathway. LPS is inserted into the OM of each cell at arate exceeding 70,000 molecules per minute (Lima et al., 2013). It isestimated that approximately one-third of LPS is modified by WaaL15 withlipid II-sourced DPP. Clearly, WaaL15 has ready access to lipid II andthis is inconsistent with a model of diffusion-limited lipid IIsequestered at the elongasome or divisome complexes. Recent evidencealso points to wider lipid II availability (Lee et al., 2014; Sham etal., 2014). The re-charging of the lipid carrier with new DPP must alsobe extremely efficient to maintain such a robust pool of PG precursor.

WaaL15 drains the available lipid II pool with no apparent detriment tocell wall integrity. Lipid II limitation can be revealed by syntheticgenetic interactions in a strain lacking the elongasome (Paradis-Bleauet al., 2014), but it is not the recharging of lipid II that islimiting, rather it is the biosynthesis of DPP. Table 1 lists somesynthetic interactions between waaL15 and mutations affecting theelongasome due to limited lipid II availability.

TABLE 1 Relevant Genes* Cotransduction Recip- Selected Fre- Donor ientAllele Gene quency yhfT3084:: waaL⁺ yhfT- mrcA::kan 85% Tn10 mrcA::kan3084::Tn10 yhfT3084:: waaL15 yhfT- mrcA::kan 89% Tn10 mrcA::kan3084::Tn10 sfsB203::Tn10 lpoA::kan waaL⁺ sfsB203::Tn10 lpoA::kan 29%sfsB203::Tn10 lpoA::kan waaL15 sfsB203::Tn10 lpoA::kan 28% zad-220::Tn10mrcB::kan waaL⁺ zad-220::Tn10 mrcB::kan 72% zad-220::Tn10 mrcB::kanwaaL15 zad-220::Tn10 mrcB::kan 13% zce-726::Tn10 lpoB::kan waaL⁺zce-726::Tn10 lpoB::kan 77% zce-726::Tn10 lpoB::kan waaL15 zce-726::Tn10lpoB::kan  5% pMurA† zad-220::Tn10 mrcB::kan waaL⁺ zad-220::Tn10mrcB::kan 79% zad-220::Tn10 mrcB::kan waaL15 zad-220::Tn10 mrcB::kan 77%zce-726::Tn10 lpoB::kan waaL⁺ zce-726::Tn10 lpoB::kan 75% zce-726::Tn10lpoB::kan waaL15 zce-726::Tn10 lpoB::kan 70% *mrcA encodes PBP1A whichfunctions with LpoA in the divisome; mrcB encodes PBP1B which functionswith LpoB in the elongasome. †Expression of murA was induced bysupplementing growth media with 100 μM IPTG.

In many bacteria, LPS is decorated with highly variable O-Ags that arelinear polymers of repeating units of 3-6 monosaccharides (Kalynych etal., 2014). In E. coli the multitude of different O-Ags initiate withGlcNAc, ECA also initiates with GlcNAc. In E. coli K-12 when colonicacid is overproduced M-LPS is made from an initiating Glc residue. TheF332S mutation broadens substrate specificity of the WaaLglycosyltransferase allowing it to efficiently accept a significantlymore bulky initiating MurNAc with an attached oligopeptide stem. Theonly other glycosyltransferase that is known to use lipid II as asubstrate is PglL from Neisseria and the use required overproduction ofthe enzyme in E. coli (Faridmoayer et al., 2008). It is also remarkablethat no OM biogenesis defect in strains carrying waaL15 is detected,demonstrating that the Lpt system is fully competent for the transportand assembly of LPS* despite the addition of both unnatural sugars andpeptide stems. Both LPS and PG are pathogen-associated molecularpatterns (PAMPs) that potently activate innate immune responses viadistinct pathways, and it seems sensible for Gram-negative bacteria tokeep these entities separated. It is expected that the F332Ssubstitution has inactivated an exclusion mechanism that prevents WaaLfrom utilizing the lipid II pool.

In certain embodiments of the invention, the present disclosure providesfor bacteria modified with the waaL15 mutation, or a bacterium modifiedto express LPS*. During production of LPS*, the Escherichia coli waaL15mutant bacteria typically produce both native LPS and the LPS*glycoform. Consequently, established “total LPS extraction” methods thathave been performed on cultures of these bacteria yield a mixture of LPSand LPS*. While this may be sufficient for some purposes, it is expectedthat other purification methods, or a combination of methods, mayprovide improved isolation and purification of the LPS* component Othermethods beyond “total LPS extraction” methods envisioned as part of thismethod include, but are not limited to, size-based chromatography thatexploits LPS*'s increased size and altered chemical composition comparedto LPS, or affinity-based methods that exploit the specific binding ofLPS* to vancomycin.

The use of LPS as an adjuvant is precluded by strong endotoxicity. LPSderivates isolated following acid and base hydrolysis have significantlyreduced endotoxicity but remain immunostimulatory. One such LPSderivative is 3-O-deacyl-4′-monophosphoryl lipid A (MPL, GSK) which ispart of the adjuvant formulation ASO4 used in the Cervarix™ humanpapillomavirus vaccine (GSK). LPS* molecules are likely sensitive toacid and base hydrolysis. It is known in the art that strains of E. colimay be engineered to produce LPS derivatives without the need a harshchemical treatment that would likely be incompatible with LPS*. It istherefore expected that introducing the waaL15 mutation into LPSderivative producing strains, such as those producing3-O-deacyl-4′-monophosphoryl lipid A, will produce a detoxified LPS*derivative that retains at least some of the immunogenic properties ofLPS*.

Certain embodiments of the invention provide for producing a modifiedlipopolysaccharide molecule that enables the molecule to activate atleast some of the immune signaling receptors and pathways of traditionalLPS and PG, including TLR4, MD2, NOD1, and NOD2 receptors, and TRIF/TRAMpathways. It is expected that applying LPS* treatment to human TLR4/MD2,NOD1, and NOD2 reporter cell lines will confirm signaling through thisreceptor and downstream pathway, and that LPS*-treated human cell lineswill show activation via the TRIF/TRAM pathway using transcriptomicanalysis.

To facilitate a better understanding of the present invention, thefollowing examples of certain aspects of some embodiments are given. Inno way should the following examples be read to limit, or define, theentire scope of the invention.

EXAMPLES Construction of Mutant Strains

Strains and plasmids used in this study are listed in Table 2 and Table3, respectively. Strains were grown in lysogeny broth (LB, Miller) orM63 minimal medium under aeration at 37° C. unless otherwise noted. Whenappropriate, media were supplemented with kanamycin (Kan, 25 μg/ml ),ampicillin (Amp, 25-125 μg/ml), tetracycline (Tet, 20 μg/ml ),chloramphenicol (Cam, 20 μg/ml ), vancomycin (Vanc, 65-260 μg/ml) andarabinose (Ara, 0.2% v/v).

Kanamycin deletion-insertion mutations of bamE, cpsG, mrcA, mrcB, lpoAand lpoB were obtained from the Keio collection (Baba et al., 2006). ECAnull rff:Tn10-66 allele was obtained from strain 21566 (Meier-Dieter etal., 1990). The ompC::Tn5 rcsC137 was obtained from strain SG20803(Brill et al., 1988). Mutant alleles were introduced by Plvirtransduction.

TABLE 2 Strain Relevant Genotype Reference MC4100 F⁻ araD139 l⁻(arg-lac)U169 rpsL150 (Casadaban, 1976) relA1 flbB5301 deoC1 ptsF25 thiNR754 MC4100 Ara⁺ (Button et al., 2007) CAG12025 F⁻ araD139 l⁻ rph-1zad-220::Tn10 (Singer et al., 1989) CAG12072 F⁻ araD139 l⁻ rph-1sfsB203::Tn10 (Singer et al., 1989) CAG12078 F⁻ araD139 l⁻ rph-1zce-726::Tn10 (Singer et al., 1989) CAG18456 F⁻ araD139 l⁻ rph-1yhfT3084::Tn10 (Singer et al., 1989) MG617 NR754 ΔlptE2::kan/plptE⁺(Maloj{hacek over (c)}ić et al., 2014) MG1029 NR754 ΔlptE2::kan/plptE613(Maloj{hacek over (c)}ić et al., 2014) MG1088 NR754 ΔlptE2::kanwaaL15/plptE613 This study MG1167 NR754 ΔlptE2 waaL15/plptE613 Thisstudy MG1180 MG1167 ΔcpsG::kan This study MG1181 MG1210 ΔbamE::kan Thisstudy MG1182 MG1211 ΔbamE::kan This study MG1196 MG1210 bamB::kan Thisstudy MG1197 MG1211 bamB::kan This study MG1210 NR754 waaL⁺ tdh::Tn10This study MG1211 NR754 waaL15 tdh::Tn10 This study MG1214 MG1167ΔcpsG::kan rff::Tn10 This study MG1234 MG1167 rff:Tn10-66 This studyMG1378 MG1210 ompC::Tn5::kan rcsC137 This study MG1379 MG1211 ompC::Tn5rcsC137 This study MG1642 NR754 waaL⁺ This study MG1643 NR754 waaL15This study MG1635 CAG12025 ΔmrcB::kan This study MG1636 CAG18456ΔmrcA::kan This study MG1671 CAG12072 ΔlpoA::kan This study MG1672CAG12078 ΔlpoB::kan This study

TABLE 3 Plasmid Description Reference plptE lptE cloned into pBAD18,Amp^(R) (Wu et al., 2006) (Kitagawa et al., pMurA ASKA plasmid withcloned murA, Cam^(R) 2006)Isolation and Identification of waaL15

Spontaneous suppressor mutants of strain MG1029 capable of growing on LBplates supplemented with vancomycin (140 μg/ml) were isolated; one suchmutant strain was MG1088. The mutation locus conferringvancomycin-resistance in MG1088 was identified by linkage mapping usinga library of random mini-Tn10 insertions (Kleckner et al., 1991). Inthis way, the tdh::Tn10 allele was found to be approximately 70% linkedto the suppressor mutation waaL15. The F332S mutation was thenidentified by PCR amplification and sequencing of the waaL locus. ThewaaL15 mutation was moved into the NR754 wild-type strain by linkagewith tdh::Tn10. In order to generate the unmarked waaL15 strain (MG1643)and its wild-type control (MG1642), the tdh::Tn10 mutation was removedfrom strains MG1210 and MG1211 by first introducing a linked ΔcysE::kanmutation (Baba et al., 2006), selecting for Kan^(R) and screening forTet^(S) transductants that were Vanc^(R) (waaL15) or Vanc^(S) (waaL+).The ΔcysE::kan mutation was then replaced with cysE+ by transduction,selection on M63 minimal medium, and screening of Vanc^(R)/Vanc^(S).

Assessment of Genetic Linkage by Co-Transduction

The genetic interaction of PG synthase mutants with waaL15 was assessedas follows. KanR-marked null alleles of lpoA, lpoB, mrcA and mrcB wereintroduced by Plvir transduction into CAG strains that carry a Tn10insertion in a nearby locus (see Table 1). Kan^(R) Tet^(R) transductantswere isolated and used to generate P1vir lysates. These P1vir were usedto transduce waaL (MG1642) or waaL15 (MG1643) strains, selecting for theTn10 marker. The frequency with which the Kan^(R)-marked lpo and mrcalleles were co-transduced (genetically linked) was determined byreplica plating on LB+Kan. Linkage was assessed in a total of 300transductants from 3 independent experiments. A decrease in thecotransduction frequency in waaL15 strains relative to waaL+indicates asynthetic interaction between waaL15 and the Kan^(R)-marked allele. Thesynthetic interaction between waaL15 and mrcB/lpoB null alleles wasrelieved in strains carrying pMurA when expression of the cloned murAgene (encoding the enzyme responsible for the first committed step inDPP biosynthesis) was induced with 100 μM isopropylβ-D-1-thiogalactopyranoside (IPTG). Overexpression of murA increases thecellular pool of UDP-MurNAc-pentapeptide and consequently also increasesthe pool of lipid II.

Analysis of LPS by SDS-PAGE and Silver Staining

A total to 1×10⁹ cells from liquid culture were taken, pelleted andresuspended 0.05 ml of ‘LPS Sample Buffer’ (0.66M Tris pH 7.6, 2% v/vsodium dodecyl sulfate [SDS], 10% v/vglycerol, 4% v/v β-mercaptoethanol,0.1% w/v bromophenol blue). Samples were boiled for 10 min and allowedto cool to room temperature. 10 gl of Proteinase K (2.5 mg/ml, in LPSSampleBuffer) was added and samples were incubated at 56° C. for 16 h.LPS samples were then resolved by SDS-PAGE and silver stained asdescribed previously (Tsai and Frasch, 1981). By quantifying banddensity using ImageJ, it was determined that LPS* constituted 29±1% ofthe total LPS in waaL15 samples.

Antibiotic Disc Diffusion Assay

3 ml of molten LB Top agar (0.75% agar) was inoculated with 0.1 ml ofovernight culture. The mixture was poured onto a LB agar plate (1.5%agar,) and allowed to set. Antibiotic discs (BD Sensi-Disc) were placedon the Top agar overlay and plates were incubated overnight at 37° C.The ‘zone of growth inhibition’ was measured across the antibiotic disc.

Fluorescence Microscopy

Overnight cultures were sub-cultured at 1:100 into fresh LB broth andgrown for 1.5 h. Al ml aliquot was taken, pelleted and was twice washedwith 1 ml M63 medium. Cells were resuspended in 0.1 ml of M63 brothcontaining 1 μg/ml of vancomycin-BODIPY-FL (LifeTechnologies, V-34850).Cells were incubated at room temperature for 10 min and then washedtwice with 1 ml M63 broth. Cells were then resuspended in 0.03 ml of M63broth, and approximately 2 ml was spotted onto an M63-agarose pad. Cellswere immediately visualized on a Nikon Eclipse 90i microscope with aNikon Plan Apo 1.4/100×Oil Ph3 phase objective.

LPS Purification

E. coli MG1210 and MG1211 were each grown in 4×1.51 LB medium shaking at37° C. overnight to stationary phase. The cells were harvested bycentrifugation for 15 min at 5,000×g, 4° C. and washed with water (700ml) and ethanol (40 ml) once, then twice with acetone (40 ml). Afterdrying the cell pellet in a desiccator overnight in vacuo, PCP(Phenol-Chloroform-petroleum ether) method was used for rough LPSextraction (Galanos et al., 1969).

PG Purification

E. coli MG1210 and MG1211 were each grown in 500 ml LB medium shaking at37° C. to stationary phase (6 h). The cell wall was isolated from theculture as described by Glauner et al., (1988) and Uehara et al.,(2009), with modifications described below. The cells were resuspendedin 20 ml phosphate buffered saline (PB, pH=7.4) and boiled for 30 min in80 ml 5% SDS. After the samples cooled, they were pelleted (14,000 rpm,25° C., 1 h) and washed six times by pelleting (14,000 rpm, 25° C., 1 h)from 50 ml water aliquots to remove the SDS. The samples wereresuspended in 1 ml PBS, treated with a-amidase (100 μl, 2 mg/ml stockin 50% glycerol, Sigma A-6380) and incubated at 37° C. with shaking for2 h. To cleave proteins attached to the cell wall, α-chymotrypsin (100μl, 3 mg/mL in 50% glycerol, Sigma C3142) was added, and the sampleswere incubated at 37° C. with shaking overnight. An additional aliquotof a-chymotrypsin (100 μl) was added, and the samples were digested foran additional 4 h. To remove the proteins, SDS was added to a finalconcentration of 1%, and the samples were incubated at 95° C. for 1 h.After cooling, the samples were again pelleted (14,000 rpm, 25° C., 1h)and washed with water repeatedly (4×25 ml) to remove the SDS. The finalpeptidoglycan (PG) samples were resuspended in 500 μL 0.02% azide andstored at 4° C.

Mutanolysin Digestion and Analysis

The PG composition was analyzed by LC/MS as previously described (Lebaret al., 2013). The method was also used to analyze LPS samples. Theglycosyl hydrolase mutanolysin liberated DPP and disaccharidetetrapeptide from LPS*. Aliquots (40 μl) of PG (from MG1210and MG1211)and LPS (from MG1210 and MG1211) were incubated with mutanolysin (10 U,2.5 μl, 4000 U/ml, Sigma M9901, stored at −20° C. in 50 mM TES, pH 7.0,1 mM MgCl2, 10% glycerol) in 50 mM sodium phosphate buffer (pH 6.0, 100μl total volume) at 37° C. with shaking overnight. Another aliquot ofmutanolysin (10 U, 2.5 μl) was added, and the mixture was incubated at37° C. with shaking for 3 h. Insoluble particles were separated bycentrifugation (16,000×g). The supernatant, containing solublefragments, was treated with sodium borohydride (10 mg/ml in water, 100μL) at room temperature for 30 min. Phosphoric acid (20%,12 μl) was thenadded to adjust pH to ˜4. When bubbling ceased, the samples werelyophilized and re-dissolved in 25 μl water, which was analyzed onLC/MS. LC/MS analysis was conducted with ESI-MS operating in positivemode. The instrument was equipped with a Waters Symmetry Shield RP18column (5 μm, 3.9×150 mm) with matching column guard. The fragments wereseparated using the following method: 0.5 ml/min H₂O (0.1% formic acid)for 5 min followed by a gradient of 0% ACN (0.1% formic acid)/H₂O (0.1%formic acid) to 20% ACN (0.1% formic acid)/H₂O (0.1% formic acid) over40 min.

Surface Plasmon Resonance Analysis

Purified LPS (0.5 mg/ml) from strains MG1210 or MG1211 were extruded in20 mMTris/HCl pH 8, 150 mM NaCl and immobilized on poly-L-lysine coatedCM3 Biacore chips on the active and reference channel, respectively(Maloj{hacek over (c)}ić et al., 2014). All experiments were performedusing a Biacore X100 instrument at 25° C. at a flow rate of 10 gl/minwith 20 mMTris/HCl pH 8, 150 mM NaCl buffer. Different concentrations ofvancomycin were injected for 400 s and dissociation was recorded foranother 500 s to return to baseline. No binding was observed to thereference channel. The equilibrium signal in the difference channel wasfitted to f=Bmax*abs(x)/(Kd+abs(x)) with R²=0.88. Standard deviation wasmeasured for 0.6 μM and 1.2 μM vancomycin in triplicate and did notexceed 1 RU.

Assessment of Vancomycin Binding Ability

The ability of purified LPS* to bind vancomycin in vitro was assessed.LPS* was immobilized on a carboxymethylated dextran (CM3) chip andsurface plasmon resonance was used to monitor interactions withdiffering concentrations of vancomycin. The specific binding ofvancomycin to LPS* was measured and a K_(d)=0.48±0.08 μM was obtained(See FIGS. 9-12), which is comparable to a reported Kd forvancomycin-lipid II interactions invesicles (Al-Kaddah et al., 2010).Clearly, LPS* molecules include high affinity binding sites forvancomycin. The ability of LPS* to directly bind vancomycin suggested apossible resistance mechanism, namely that vancomycin is titratedoutside the cell. To test this hypothesis, weperformed live cellmicroscopy using a fluorescent vancomycin-BODIPY. A wild-type strainbackground with an intact OM that prevents the influx of vancomycin wasused, to avoid labeling intracellular sites of PG synthesis. Indeed,waaL+ cells could not be fluorescently labeled (See FIG. 13). On theother hand, circumferential labeling of waaL15 bacteria was readilydetected, confirming the presence of accessible D-Ala-D-Ala residues atthe cell surface (See FIG. 13).

Comparative Analysis of LPS* and LPS

Traditional adjuvants (e.g. aluminum salts) are potently immunogenic butproduce a biased immune response. Specifically, these adjuvants are poorat eliciting a TH1 response to vaccine components. Activation of TH1responses is important for generating protective antibacterial andantiviral immunity against many pathogens. It is established that theadjuvant effect of LPS produces a TH1-biased immunity. It is alsoestablished that LPS-stimulated immune signaling pathways aresynergistically activated when provided with additional stimulation withNOD ligands (PG components). By utilizing reporter human cell lines toquantify the strength of immune activation, including activation viaTLR4/MD2, NOD1 and NOD2 receptors, the LPS* immune response can becompared to LPS via transcriptomic analysis. The production of immuneeffector molecules (including cytokines and chemokines) can becharacterized using commercially available protein detection assays. Itis expected that LPS* will provide more robust immune activation, orresult in a distinct profile of immune responses (e.g. biased toTH1-type immunity) and/or distinct production of effector molecules(including cytokines and chemokines) in comparison to LPS, owing toactivation of TLR4 and NOD1/2 signaling.

Assessing the Adjuvant Properties of LPS* and Derivative Molecules

The ability of LPS* and its derivatives to elicit protective immunitycan be assessed by using these molecules as part of an adjuvantformulation in vaccinations or using model antigens. In one example,mice can be immunized against the ovalbumin antigen by vaccination withformulations where the adjuvant is either an LPS* derivative, or an LPSderivative or alum. The immune response of these mice to vaccinationscan be assessed and compared. In another example, the ability of LPS* toelicit protective immunity can be assessed using model pathogens. Micecan be immunized against pathogen antigens by vaccinations formulatedwith LPS*-based, LPS-based, or alum-based adjuvants. Mice can then bechallenged with the pathogen and survival will be recorded and comparedto LPS. It is expected that LPS* and its derivatives will provide morerobust immunity or result in an altered immunity that improves theefficacy of immunization, compared to LPS and its derivatives.

SEQUENCE LISTING <110> Silhavy, Thomas J. Grabowicz, MarcinKahne, Daniel <120>Modified Lipopolysaccharide Glycoform and Method of Use <160>NUMBER OF SEQ ID NOS: 2 <210> SEQ ID NO 1 <211> LENGTH: 419 <212>TYPE: PRT <213> ORGANISM: Escherichia coli <400> SEQUENCE: 1mltsfklhsl kpytlkssmi leiityilcf fsmiiafvdn tfsikiynit aivcllslil  60rgrqenynik nlilplsifl iglldliwys afkvdnspfr atyhsylnta kififgsfiv 120fltltsqlks kkesvlytly slsfliagya myinsihend risfgvgtat gaaystmlig 180ivsgvailyt kknhpflfll nscavlyvla ltqtratlll fpiicvaali ayynkspkkf 240tssivlliai lasiviifnk piqnryneal ndlnsytnan svtslgarla myeiglnifi 300kspfsfrsae sraesmnllv aehnrlrgal essnvhlhne iieagslkgl mgifstlfly 360fslfyiaykk ralglliltl givgiglsdv iiwarsipii iisaivlllv innrnntin 419<210> SEQ ID NO 2 <211> LENGTH: 419 <212> TYPE: PRT <213>ORGANISM: Escherichia coli <400> SEQUENCE: 2mltsfklhsl kpytlkssmi leiityilcf fsmiiafvdn tfsikiynit aivcllslil  60rgrqenynik nlilplsifl iglldliwys afkvdnspfr atyhsylnta kififgsfiv 120fltltsqlks kkesvlytly slsfliagya myinsihend risfgvgtat gaaystmlig 180ivsgvailyt kknhpflfll nscavlyvla ltqtratlll fpiicvaali ayynkspkkf 240tssivlliai lasiviifnk piqnryneal ndlnsytnan svtslgarla myeiglnifi 300kspfsfrsae sraesmnllv aehnrlrgal efsnvhlhne iieagslkgl mgifstlfly 360fslfyiaykk ralglliltl givgiglsdv iiwarsipii iisaivlllv innrnntin 419

What is claimed is:
 1. A mutant O-antigen ligase comprising an isolated protein that has the amino acid sequence SEQ ID NO:
 1. 2. A mutant O-antigen ligase comprising an isolated protein having at least 90% sequence identity to SEQ ID NO: 2 and having an amino acid substitution of phenylalanine to serine at the phenylalanine homologous to position 332 of SEQ ID NO:
 2. 3. A vaccine adjuvant comprising a lipopolysaccharide isolated from the mutant O-antigen ligase of claim 1 or
 2. 4. A vaccine adjuvant comprising a lipopolysaccharide derivative isolated from the mutant O-antigen ligase of claim 1 or
 2. 5. A polynucleotide comprising a polynucleotide sequence encoding the mutant O-antigen ligase of claim 1 or
 2. 6. A lipopolysaccharide glycoform modified with peptidoglycan cell wall fragments.
 7. The lipopolysaccharide glycoform of claim 6, wherein the lipopolysaccharide glycoform is adapted to display antibiotic-specific binding sites at a cell surface.
 8. The lipopolysaccharide glycoform of claim 7, wherein the antibiotic is vancomycin.
 9. The lipopolysaccharide glycoform of claim 6 or 7, wherein the lipopolysaccharide glycoform is adapted to activate at least one receptor within a human body.
 10. The lipopolysaccharide glycoform of claim 9, wherein the at least one receptor is a TRL4 receptor.
 11. The lipopolysaccharide glycoform of claim 9, wherein the at least one receptor is a MD2 receptor.
 12. The lipopolysaccharide glycoform of claim 9, wherein the at least one receptor is a NOD1 receptor.
 13. The lipopolysaccharide glycoform of claim 9, wherein the at least one receptor is a NOD2 receptor.
 14. The lipopolysaccharide glycoform of claim 6 or 7, wherein the lipopolysaccharide glycoform is adapted to activate at least one signaling pathway.
 15. The lipopolysaccharide glycoform of claim 14, wherein the at least one signaling pathway is the TRIF pathway.
 16. The lipopolysaccharide glycoform of claim 14, wherein the at least one signaling pathway is the TRAM pathway.
 17. A bacterium that expresses a lipopolysaccharide glycoform of claim
 6. 18. The bacterium of claim 17, wherein the bacteria comprises a gene encoding a ligase with the mutation of claim 1 or
 2. 19. A method for generating an LPS molecule comprising the steps of: providing an E. coli strain adapted to express the mutant O-antigen ligase of claim 1 or 2; growing the E. coli strain; and isolating the LPS molecule.
 20. The method of claim 19, wherein isolating the LPS molecule comprises separating the LPS molecules based on at least one of the group consisting of size, chemical composition, and affinity for a particular binding agent.
 21. A method for generating a LPS* derivative molecule having reduced endotoxicity and improved immunogenicity comprising the steps of: providing an E. coli strain adapted to express a LPS derivative molecule having reduced endotoxicity compared to a LPS molecule that the LPS derivative molecule is derived from; modifying the E. coli strain by creating a mutant 0-antigen ligase accord to claim 1 or 2; and allowing the modified E. coli strain to grow under conditions to produce a LPS* derivative molecule having reduced endotoxic compared to the LPS molecule the LPS* derivative molecule is dervived from and improved immunogenicity compared to the derivative LPS molecule the LPS* derivative molecule is derived from.
 22. The method for generating a LPS* derivative molecule of claim 21, further comprising isolating the LPS* derivative molecule.
 23. The method for generating a LPS* derivative molecule of claim 21, wherein the first LPS derivative molecule is 3-O-deacyl-4′-monophosphoryl lipid A.
 24. A vaccine adjuvant comprising a lipopolysaccharide derivative molecule having reduced endotoxicity and improved immunogenicity of claim
 21. 25. A modified lipopolysaccharide molecule having at least one non-native sugar and a greater molecular weight as compared to the lipopolysaccharide molecule it is modified from. 